65 Placental Function at Term is Altered in Broodmares Fed with Cereals from Mid Gestation

2018 ◽  
Vol 30 (1) ◽  
pp. 171
Author(s):  
M. Robles ◽  
P. Peugnet ◽  
C. Dubois ◽  
F. Piumi ◽  
L. Jouneau ◽  
...  
Keyword(s):  
Random Effect ◽  
Area Under The Curve ◽  
Enrichment Analysis ◽  
Mixed Linear Model ◽  
Tolerance Test ◽  
Gene Set Enrichment Analysis ◽  
Acid Oxidation ◽  
Placental Function ◽  
Insulin Resistant ◽  
Gene Sets

Recent data obtained in our laboratory suggest that feeding pregnant broodmares with cereal concentrates may affect both mare and foal metabolism in the short and long term. Here, we investigated feto-placental biometry and placental function at term in mares fed with cereals and forage or forage only. Twenty-two multiparous mares inseminated with the same stallion were allocated to 1 of 2 groups from 7 months of gestation: group F (n = 10) were fed forage only, whereas group B (n = 12) received forage and cracked barley until foaling. At 3 and 9 months of gestation, a glucose tolerance test (IVGTT) was performed to evaluate the insulin resistance of pregnant mares. At birth, placentas and foals were weighed and measured. Placental samples were collected above the umbilical cord insertion and snap frozen. An RNA sequencing (RNAseq) analysis was performed on 9 placentas of each group. After normalization, gene levels were analysed using the DESEqn 2 package of R software (https://www.r-project.org/). Enrichment of gene sets was analysed using the Gene Set Enrichment Analysis (GSEA) software using the Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Gene Ontology [GO, biological processes (bp), molecular function (mf) and cellular components (cc)] databases. Gene analysis statistical results were considered significant for P-values < 0.05 after false rate discovery (fdr) correction. The IVGTT results were analysed using a type 3 ANOVA on a mixed linear model with group as fixed effect and age of the mare as random effect. At 3 months of gestation, maternal glucose metabolism was not different between groups. At 9 months, B mares had a higher insulin area under the curve (AUC) after glucose injection than F mares (P < 0.01), without any difference in glucose AUC, suggesting that B mares were more insulin resistant than F mares. At birth, no difference was observed for feto-placental biometry between groups. Gene-level analysis could not discern differences in gene expression between groups after fdr correction. The GSEA analysis, however, showed that 8 gene sets were down-regulated in C placentas (2 KEGG, 2 GObp, 3 GOmf, 1 GOcc) and 193 gene sets were up-regulated (15 KEGG, 144 GObp, 12 GOmf, 22 GOcc) in B placentas. The down-regulated gene sets were involved in neutral amino acids and anion transport, fatty acid oxidation, acetyl coA synthesis, cholesterol and folate degradation, and the up-regulated gene sets were involved in RNA expression, inflammation (activation and recruitment of immune cells, MAPK signalling, complement and coagulation cascades, pro-inflammatory cytokine production and signalling) and in vascularisation (vasculogenesis, angiogenesis and smooth muscle cells development). The results are consistent with the altered function observed in term placentas of women who suffer from gestational diabetes. In conclusion, feeding pregnant mares with cereal from mid gestation alters the placental function at term. The authors thank the GeT platform (Toulouse, France) for the sequencing of the samples.

scholarly journals TFEA.ChIP: A tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets

2018 ◽  
Author(s):  
Laura Puente-Santamaria ◽  
Luis del Peso
Keyword(s):  
Transcription Factors ◽  
Web Application ◽  
Area Under The Curve ◽  
Enrichment Analysis ◽  
Cell Types ◽  
Gene Set Enrichment Analysis ◽  
Link Type ◽  
Gene Sets ◽  
Wide Range ◽  
Depth Analysis

AbstractThe identification of transcription factors (TFs) responsible for the co-regulation of specific sets of genes is a common problem in transcriptomics. Herein we describe TFEA.ChIP, a tool to estimate and visualize TF enrichment in gene lists representing transcriptional profiles. To generate the gene sets representing TF targets, we gathered ChIP-Seq experiments from the ENCODE Consortium and GEO datasets and used the correlation between Dnase Hypersensitive Sites across cell lines to generate a database linking TFs with the genes they interact with in each ChIP-Seq experiment. In its current state, TFEA.ChIP covers 327 different transcription factors from 1075 ChIP-Seq experiments, with over 150 cell types being represented. TFEA.ChIP accepts gene sets as well as sorted lists differentially expressed genes to compute enrichment scores for each of the datasets in its internal database using an Fisher’s exact association test or a Gene Set Enrichment Analysis. We validated TFEA.ChIP using a wide variety of gene sets representing signatures of genetic and chemical perturbations as input and found that the relevant TF was correctly identified in 103 of a total of 144 analyzed datasets with a median area under the curve (AUC) of 0.86. In depth analysis of an RNAseq dataset, illustrates that the use of ChIP-Seq data instead of PWM-based provides key biological context to interpret the results of the analysis. To facilitate its integration into transcriptome analysis pipelines and allow easy expansion and customization of the TF-gene database, we implemented TFEA.ChIP as an R package that can be downloaded from Bioconductor: https://www.bioconductor.org/packages/devel/bioc/html/TFEA.ChIP.html and github: https://github.com/LauraPS1/TFEA-drafts In addition, make it available to a wide range of researches, we have also developed a web application that runs the package from the server side and enables easy exploratory analysis through interactive graphs: https://www.iib.uam.es/TFEA.ChIP/

scholarly journals Higher Acid-Base Imbalance Associated with Respiratory Failure Could Decrease the Survival of Patients with Scrub Typhus during Intensive Care Unit Stay: A Gene Set Enrichment Analysis

2019 ◽  
Vol 8 (10) ◽  
pp. 1580 ◽  
Author(s):  
Kyoung Min Moon ◽  
Kyueng-Whan Min ◽  
Mi-Hye Kim ◽  
Dong-Hoon Kim ◽  
Byoung Kwan Son ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Intensive Care ◽  
Respiratory Failure ◽  
Scrub Typhus ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Acid Base ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Gene Sets

Ninety percent of patients with scrub typhus (SC) with vasculitis-like syndrome recover after mild symptoms; however, 10% can suffer serious complications, such as acute respiratory failure (ARF) and admission to the intensive care unit (ICU). Predictors for the progression of SC have not yet been established, and conventional scoring systems for ICU patients are insufficient to predict severity. We aimed to identify simple and robust indicators to predict aggressive behaviors of SC. We evaluated 91 patients with SC and 81 non-SC patients who were admitted to the ICU, and 32 cases from the public functional genomics data repository for gene expression analysis. We analyzed the relationships between several predictors and clinicopathological characteristics in patients with SC. We performed gene set enrichment analysis (GSEA) to identify SC-specific gene sets. The acid-base imbalance (ABI), measured 24 h before serious complications, was higher in patients with SC than in non-SC patients. A high ABI was associated with an increased incidence of ARF, leading to mechanical ventilation and worse survival. GSEA revealed that SC correlated to gene sets reflecting inflammation/apoptotic response and airway inflammation. ABI can be used to indicate ARF in patients with SC and assist with early detection.

scholarly journals Drug perturbation gene set enrichment analysis (dpGSEA): a new transcriptomic drug screening approach

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Mike Fang ◽  
Brian Richardson ◽  
Cheryl M. Cameron ◽  
Jean-Eudes Dazard ◽  
Mark J. Cameron
Keyword(s):  
Drug Targets ◽  
T Regulatory Cells ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Regulatory Cells ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Gene Sets ◽  
Gastroenteropancreatic Neuroendocrine Tumor ◽  
Public Datasets

Abstract Background In this study, we demonstrate that our modified Gene Set Enrichment Analysis (GSEA) method, drug perturbation GSEA (dpGSEA), can detect phenotypically relevant drug targets through a unique transcriptomic enrichment that emphasizes biological directionality of drug-derived gene sets. Results We detail our dpGSEA method and show its effectiveness in detecting specific perturbation of drugs in independent public datasets by confirming fluvastatin, paclitaxel, and rosiglitazone perturbation in gastroenteropancreatic neuroendocrine tumor cells. In drug discovery experiments, we found that dpGSEA was able to detect phenotypically relevant drug targets in previously published differentially expressed genes of CD4+T regulatory cells from immune responders and non-responders to antiviral therapy in HIV-infected individuals, such as those involved with virion replication, cell cycle dysfunction, and mitochondrial dysfunction. dpGSEA is publicly available at https://github.com/sxf296/drug_targeting. Conclusions dpGSEA is an approach that uniquely enriches on drug-defined gene sets while considering directionality of gene modulation. We recommend dpGSEA as an exploratory tool to screen for possible drug targeting molecules.

Robust Metabolic Transcriptional Components in 34,494 Patient-Derived Samples and Cell Lines

2021 ◽  
Author(s):  
Vincent Christiaan Leeuwenburgh ◽  
Carlos G. Urzúa-Traslaviña ◽  
Arkajyoti Bhattacharya ◽  
Marthe T.C. Walvoort ◽  
Mathilde Jalving ◽  
...  
Keyword(s):  
Cell Lines ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Metabolic Processes ◽  
Gene Sets ◽  
Transcriptional Changes ◽  
Cancer Tissues ◽  
Tumor Biopsies ◽  
Transcriptional Landscape

Abstract Background: Patient-derived bulk expression profiles of cancers can provide insight into transcriptional changes that underlie reprogrammed metabolism in cancer. These profiles represent the average expression pattern of all heterogeneous tumor and non-tumor cells present in biopsies of tumor lesions. Hence, subtle transcriptional footprints of metabolic processes can be concealed by other biological processes and experimental artifacts. However, consensus Independent Component Analyses (c-ICA) can capture statistically independent transcriptional footprints, of both subtle and more pronounced metabolic processes. Methods: We performed c-ICA with 34,494 bulk expression profiles of patient-derived tumor biopsies, non-cancer tissues, and cell lines. Gene set enrichment analysis with 608 gene sets that describe metabolic processes was performed to identify transcriptional components enriched for metabolic processes (mTCs). The activity of these mTCs were determined in all samples to create a metabolic transcriptional landscape. Results: A set of 555 mTCs were identified of which many were robust across different datasets, platforms, and patient-derived tissues and cell lines. We demonstrate how the metabolic transcriptional landscape defined by the activity of these mTCs in samples can be used to explore associations between the metabolic transcriptome and drug sensitivities, patient outcomes, and the composition of the immune tumor microenvironment. Conclusions: To facilitate the use of our transcriptional metabolic landscape, we have provided access to all data via a web portal ( www.themetaboliclandscapeofcancer.com ). We believe this resource will contribute to the formulation of new hypotheses on how to metabolically engage the tumor or its (immune) microenvironment.

scholarly journals Weighted Kolmogorov Smirnov testing: an alternative for Gene Set Enrichment Analysis

2015 ◽  
Vol 14 (3) ◽  
Author(s):  
Konstantina Charmpi ◽  
Bernard Ycart
Keyword(s):  
Weight Function ◽  
Null Hypothesis ◽  
Computing Time ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Test Statistic ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Gene Sets ◽  
Kolmogorov Smirnov

AbstractGene Set Enrichment Analysis (GSEA) is a basic tool for genomic data treatment. Its test statistic is based on a cumulated weight function, and its distribution under the null hypothesis is evaluated by Monte-Carlo simulation. Here, it is proposed to subtract to the cumulated weight function its asymptotic expectation, then scale it. Under the null hypothesis, the convergence in distribution of the new test statistic is proved, using the theory of empirical processes. The limiting distribution needs to be computed only once, and can then be used for many different gene sets. This results in large savings in computing time. The test defined in this way has been called Weighted Kolmogorov Smirnov (WKS) test. Using expression data from the GEO repository, tested against the MSig Database C2, a comparison between the classical GSEA test and the new procedure has been conducted. Our conclusion is that, beyond its mathematical and algorithmic advantages, the WKS test could be more informative in many cases, than the classical GSEA test.

scholarly journals Gastroesophageal reflux activates the NF-κB pathway and impairs esophageal barrier function in mice

2013 ◽  
Vol 305 (1) ◽  
pp. G58-G65 ◽  
Author(s):  
Yu Fang ◽  
Hao Chen ◽  
Yuhui Hu ◽  
Zorka Djukic ◽  
Whitney Tevebaugh ◽  
...  
Keyword(s):  
Gastroesophageal Reflux ◽  
Barrier Function ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Esophageal Epithelium ◽  
Gene Set Enrichment ◽  
Gene Sets ◽  
Epithelial Resistance

The barrier function of the esophageal epithelium is a major defense against gastroesophageal reflux disease. Previous studies have shown that reflux damage is reflected in a decrease in transepithelial electrical resistance associated with tight junction alterations in the esophageal epithelium. To develop novel therapies, it is critical to understand the molecular mechanisms whereby contact with a refluxate impairs esophageal barrier function. In this study, surgical models of duodenal and mixed reflux were developed in mice. Mouse esophageal epithelium was analyzed by gene microarray. Gene set enrichment analysis showed upregulation of inflammation-related gene sets and the NF-κB pathway due to reflux. Significance analysis of microarrays revealed upregulation of NF-κB target genes. Overexpression of NF-κB subunits (p50 and p65) and NF-κB target genes (matrix metalloproteinases-3 and -9, IL-1β, IL-6, and IL-8) confirmed activation of the NF-κB pathway in the esophageal epithelium. In addition, real-time PCR, Western blotting, and immunohistochemical staining also showed downregulation and mislocalization of claudins-1 and -4. In a second animal experiment, treatment with an NF-κB inhibitor, BAY 11-7085 (20 mg·kg−1·day−1 ip for 10 days), counteracted the effects of duodenal and mixed reflux on epithelial resistance and NF-κB-regulated cytokines. We conclude that gastroesophageal reflux activates the NF-κB pathway and impairs esophageal barrier function in mice and that targeting the NF-κB pathway may strengthen esophageal barrier function against reflux.

Cetuximab-induced skin rash: A molecular map relating polymorphisms, cell-adhesion, and autoimmunity.

2015 ◽  
Vol 33 (3_suppl) ◽  
pp. 570-570
Author(s):  
Sebastian Schaaf ◽  
Matthias Froelich ◽  
Thomas Kirchner ◽  
Volker Heinemann ◽  
Andreas Jung ◽  
...  
Keyword(s):  
Cell Adhesion ◽  
Skin Rash ◽  
Enrichment Analysis ◽  
Inhibitory Effect ◽  
Gene Set Enrichment Analysis ◽  
Inhibitory Antibody ◽  
Molecular Map ◽  
Gene Sets ◽  
Starting Point ◽  
The One

570 Background: Colorectal cancer (CRC) treatment with the EGFR-inhibitory antibody Cetuximab (CTX) is known to cause skin rashes (SR) of varying degree in most patients. Severity of SR is positively associated with tumor response. The underlying molecular mechanism linking both effects is still unknown. Detangling its genetic background would allow a simultaneous understanding of SR and response. Stratification of patients based on the related polymorphisms (PMs) is of clinical relevance. Methods: A systematic literature review was performed to develop a molecular map which incorporates specific pathways related to cancer, CTX specific mechanisms of action, skin rash, and autoimmunity. Exome data was generated from blood samples of 23 KRAS wild type patients taken prior to CTX treatment. Under CTX, eleven of the 23 patients showed SR of grades 3-4, twelve reacted with a grade 1 SR. Differential somatic PMs were analyzed between both groups. A gene set enrichment analysis for the imbalanced PMs was performed against gene sets of our molecular map. Imbalance was stated if at least seven patients more in the one group compared to the other carried this specific PM. Results: A total of 591 genes containing imbalanced PMs were found. Bioinformatic validation focused on the following findings of potential clinical interest: (1) PMs in genes specifically related to cell adhesion (CDH1, LAMC1, FBN2, NCAM1) or its regulation (WNT9B), (2) to autoimmunity (CXCL16, ADAM12, OS9, DOCK2), (3) in the central regulator TP53, (4) in genes playing a role in immunity and cell adhesion (DOCK2 and THBS2). PMs in the mentioned genes enabled to discriminate patients with and without severe skin rash. Validation of these findings is needed based on new independent CTX treated patients. Conclusions: Our findings suggest that genomic predisposition may exist which interact with CTX treatment by inducing alteration of cell adhesion. Altering adhesion between tumor cells makes them more accessible to the EGFR-inhibitory effect of CTX. Altering cell adhesion between epithelial cells introduces the acne like phenotypes of skin rash, presumably via the mechanism of epithelial activation. This will be the starting point for further research.

Differential gene expression in prostate tissue according to vasectomy.

2016 ◽  
Vol 34 (2_suppl) ◽  
pp. 298-298
Author(s):  
Kathryn M Wilson ◽  
Travis Gerke ◽  
Ericka Ebot ◽  
Jennifer A Sinnott ◽  
Jennifer R. Rider ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Cancer Diagnosis ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Prostate Tissue ◽  
Gene Set Enrichment ◽  
Normal Prostate ◽  
Gene Sets ◽  
Normal Prostate Tissue

298 Background: We previously found that vasectomy was associated with an increased risk of prostate cancer, and particularly, risk of lethal prostate cancer in the Health Professionals Follow-up Study (HPFS). However, the possible biological basis for this finding is unclear. In this study, we explored possible biological mechanisms by assessing differences in gene expression in the prostate tissue of men with and without a history of vasectomy prostate cancer diagnosis. Methods: Within the HPFS, vasectomy data and gene expression data (20,254 genes) was available from archival tumor tissue from 263 cases, 124 of whom also had data for adjacent normal tissue. To relate expression of individual genes to vasectomy we used linear regression adjusting for age and year at diagnosis. We ran gene set enrichment analysis to identify pathways of genes associated with vasectomy. Results: Among 263 cases, 67 (25%) reported a vasectomy prior to cancer diagnosis. Mean age at diagnosis was 66 years among men without and 65 years among men with vasectomy. Median time between vasectomy and prostate cancer diagnosis was 25 years. Gene expression in tumor tissue was not associated with vasectomy status. In adjacent normal tissue, three individual genes were associated with vasectomy with Bonferroni-corrected p-values of < 0.10: RAPGEF6, OR4C3, and SLC35F4. Gene set enrichment analysis found five pathways upregulated and seven pathways downregulated in men with vasectomy compared to those without in normal prostate tissue with a FDR < 0.05. Upregulated pathways included several immune-related gene sets and G-protein-coupled receptor gene sets. Conclusions: We identified significant differences in gene expression profiles in normal prostate tissue according to vasectomy status among men treated for prostate cancer. The fact that such differences existed several decades after vasectomy provides support for the idea that vasectomy may play a role in the etiology of prostate cancer.

Time course-dependent changes in the transcriptome of human skeletal muscle during recovery from endurance exercise: from inflammation to adaptive remodeling

2014 ◽  
Vol 116 (3) ◽  
pp. 274-287 ◽  
Author(s):  
Oliver Neubauer ◽  
Surendran Sabapathy ◽  
Kevin J. Ashton ◽  
Ben Desbrow ◽  
Jonathan M. Peake ◽  
...  
Keyword(s):  
Gene Expression ◽  
Skeletal Muscle ◽  
Endurance Exercise ◽  
Time Course ◽  
Acute Stress ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Matrix Remodeling ◽  
Molecular Signatures ◽  
Gene Sets

Reprogramming of gene expression is fundamental for skeletal muscle adaptations in response to endurance exercise. This study investigated the time course-dependent changes in the muscular transcriptome after an endurance exercise trial consisting of 1 h of intense cycling immediately followed by 1 h of intense running. Skeletal muscle samples were taken at baseline, 3 h, 48 h, and 96 h postexercise from eight healthy, endurance-trained men. RNA was extracted from muscle. Differential gene expression was evaluated using Illumina microarrays and validated with qPCR. Gene set enrichment analysis identified enriched molecular signatures chosen from the Molecular Signatures Database. Three hours postexercise, 102 gene sets were upregulated [family wise error rate (FWER), P < 0.05], including groups of genes related with leukocyte migration, immune and chaperone activation, and cyclic AMP responsive element binding protein (CREB) 1 signaling. Forty-eight hours postexercise, among 19 enriched gene sets (FWER, P < 0.05), two gene sets related to actin cytoskeleton remodeling were upregulated. Ninety-six hours postexercise, 83 gene sets were enriched (FWER, P < 0.05), 80 of which were upregulated, including gene groups related to chemokine signaling, cell stress management, and extracellular matrix remodeling. These data provide comprehensive insights into the molecular pathways involved in acute stress, recovery, and adaptive muscular responses to endurance exercise. The novel 96 h postexercise transcriptome indicates substantial transcriptional activity potentially associated with the prolonged presence of leukocytes in the muscles. This suggests that muscular recovery, from a transcriptional perspective, is incomplete 96 h after endurance exercise involving muscle damage.

scholarly journals Oxandrolone Enhances Hepatic Ketogenesis in Adult Men

2008 ◽  
Vol 56 (7) ◽  
pp. 920-924 ◽  
Author(s):  
Gloria Lena Vega ◽  
Jacob J. Clarenbach ◽  
Fredrick Dunn ◽  
Scott M. Grundy
Keyword(s):  
Fatty Acids ◽  
Hepatic Lipase ◽  
Area Under The Curve ◽  
Density Lipoprotein ◽  
Tolerance Test ◽  
Acid Oxidation ◽  
Short Term ◽  
Nonesterified Fatty Acids ◽  
Term Administration ◽  
Plasma High Density

BackgroundImmediate administration of oxandrolone markedly increases hepatic lipase activity and reduces levels of plasma high-density lipoprotein.Rationale for the studyWe postulated that oxandrolone should increase hepatic lipase and that the nonesterified fatty acids generated would enhance hepatic ketogenesis during an extended fat tolerance test.Main ResultsEighteen men participated in the study using short-term administration of oxandrolone (10 mg/d) over a week. Subjects had evaluation of hepatic ketogenesis at baseline and after 7 days of administration of oxandrolone. Ketogenesis was assessed by measuring plasma levels of 3-hydroxybutyrate during a fat tolerancetest. Oxandrolone increased fasting levels of 3-hydroxybutyrate by 70%, and increased the area under the curve during an FFT by 53% above pretreatment levels without affecting the areas under the curve for nonesterified fatty acids, glycerol, or triglycerides. Fasting 3-hydroxybutyrate levels correlated with nonesterified fatty acids and with triglycerides; however, there were no significant correlations with any other parameter.ConclusionsThis study shows that short-term administration of oxandrolone results in marked increases in hepatic ketogenesis. This finding is consistent with an increased influx of fatty acids into the liver secondary to lipoprotein lipolysis by increased hepatic lipase. However, the possibility cannot be ruled out that oxandrolone acts directly in the liver to stimulate fatty acid oxidation. Therefore, the observation of increased ketogenesis will require further studies to determine the molecular basis of the response.

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